Wednesday’s long-anticipated move by Egyptian security forces to violently clear a pair of Muslim Brotherhood protest sites in the capital was aimed at ending an impasse that had politically crippled the country. But the violence of the crackdown, which has led to hundreds of casualties, has paved the way for more chaos and instability in Egypt.

The Ministry of Health estimated the total number of dead at 278, including security-forces fatalities, but that figure is expected to rise overnight. As the fighting continued throughout the day, several Coptic churches around the country were attacked and damaged in a possible wave of Brotherhood reprisals.

Minister of Interior Mohamed Ibrahim told reporters on Wednesday evening that security forces had followed orders and employed admirable restraint. He claimed that dozens of illegal firearms — including automatic weapons — had been discovered in the Brotherhood protest site. Ibrahim made it clear that the days of the Brotherhood occupying public spaces in protest had come to an end. “We will not allow any other sit-in in any square in any place in the country,” he said.

In an e-mail to TIME, Major General Mohamed Elkeshky — a longtime Egyptian military attaché in Washington and a member of the Supreme Council of the Armed Forces — argued the necessity of the raids, saying the Brotherhood protest sites had become a threat to national unity and a dangerous nuisance for area residents. “The sit-in has infringed the rights of all residence[sic] of the area, and has been building walls, accumulating weapons, using children and women as human shields, affecting extremely negatively the hygienic situation in the area and negatively affecting the life of the residence[sic],” Elkeshky wrote. “The Egyptian security forces continue to maintain self-control and respect of human rights, in its efforts to maintain peace and security in Egypt.”

But some prominent figures within the military-backed transitional government of interim President Adly Mansour — who announced today a monthlong state of emergency and a curfew in place in Cairo and 10 other governorates — aren’t buying the narrative invoked by security officials. As security forces continued to lay siege with live ammunition, Mansour’s fledgling governing coalition began splintering with the resignation of Vice President Mohamed ElBaradei. “It has become difficult for me to hold responsibility for decisions that I do not agree with, whose consequences I fear,” ElBaradei said in a public statement. “I cannot be responsible for one drop of blood in front of God, and then in front of my conscience, especially with my faith that we could have avoided it.”

ElBaradei’s resignation removes one of the Mansour government’s most high-profile statesmen and international advocates. A Nobel Peace Prize recipient, ElBaradei has put his revolutionary credentials and reputation on the line for the past six weeks — defending the military’s July 3 intervention as necessary to save the country from disaster under then President Mohamed Morsi and the Muslim Brotherhood. In subsequent interviews, he cast himself as an internal check within the new government who was pushing for dialogue and compromise while holding the hawks calling for a crackdown at bay.

For the transitional government now, ElBaradei’s diplomatic skill might be more needed than ever, as Wednesday’s bloody dispersal of the sites prompted angry reactions from around the world, including even the Obama Administration — which “strongly condemned” the violence and added: “We also strongly oppose a return to a state-of-emergency law, and call on the government to respect basic human rights such as freedom of peaceful assembly and due process under the law. The world is watching what is happening in Cairo.”

In separate comments to reporters, White House spokesman Josh Earnest was even more direct. “There’s no ambiguity … about the importance of respecting basic human rights,” he said. “That has been communicated to the Egyptians on a range of levels … It’s time for them to get back on a path of respecting the basic human rights of their people.”

These are stronger words than usual for the Obama Administration, which struggled for weeks to avoid publicly labeling the military intervention a “coup,” then seemed to side with the military-backed government last week when Secretary of State John Kerry went on record as saying Morsi’s ouster was aimed at “restoring democracy” in Egypt. But Earnest declined to comment on whether Washington’s disapproval will affect the $1.3 billion in annual American aid that Egypt receives each year. So far the Administration’s actions in that regard — such as the recent delay of a shipment of F-16 fighters and revelations today that it may scrap a planned joint military exercise with Egypt — have remained largely symbolic.

The offensive started just before 7 a.m. on Wednesday, launched against a pair of sites where Morsi supporters have gathered for weeks demanding his reinstatement. Within hours, the area around the Nahda Square sit-in, outside the gates of Cairo University, were a maze of burning tires and smoldering tents. But the Nahda camp was always the smaller and more tenuous of the two Brotherhood sites. The primary protest site — across town at the Rabaa Adaweya mosque in Cairo’s Nasr City district — represented a much more complicated security challenge.

There, tens of thousands of Brotherhood supporters have been entrenched for more than six weeks — since several days before Morsi was ousted. Morsi was deposed by the military on July 3 in response to unprecedented nationwide protests demanding his ouster just one year after he became Egypt’s first democratically elected civilian President.

The Rabaa site is heavily fortified — albeit with makeshift barricades that couldn’t withstand an armored assault. Protesters there managed to keep their numbers robust through the Muslim fasting period of Ramadan, which recently ended, and their ranks swelled further in recent days as government ultimatums made it clear the crackdown was imminent. All told, their sit-in lasted far longer than the 18 days of massed protests in Tahrir Square that brought down the dictatorial regime of President Hosni Mubarak in February 2011.

All through the day on Wednesday, security forces laid siege to the Rabaa site. Witnesses on the scene reported heavy use of live ammunition; journalists attempting to approach the sit-in area have been fired upon, with at least two journalists confirmed killed. Those inside Rabaa reported taking regular sniper fire from surrounding rooftops.

By nightfall, about 12 hours after the assault started, security forces managed to penetrate deep into the heart of the sit-in and largely disperse it, amid reports that senior Brotherhood officials had been captured. Among the dead are a cameraman for the Sky News channel and the 17-year-old daughter of senior Brotherhood official Mohammed al-Beltagy.

If the government does succeed in physically repressing the Brotherhood, it would represent a new crossroads for the Egyptian postrevolutionary experiment — one where each potential path forward offers a political reality distant from what a euphoric Egypt imagined possible after the fall of Mubarak in 2011.

Interim President Mansour’s military-backed government can now end the crippling national stalemate between the Brotherhood and most other political forces and get on with the business of organizing a new transitional road map — including new parliamentary and presidential elections extending into next year. It’s unclear how smooth a transition to democracy the government can achieve in the current moment of curfews and a state of emergency.

A full Brotherhood purge from public and political life, which seems likely at this point, would drive the venerable and still powerful Islamist organization back underground — where it spent decades of its existence before the 2011 revolution. It would be an embittered, aggrieved faction, emboldened by the memories of its adherents’ recent sacrifices and the knowledge that it won every postrevolutionary election it entered. If the military’s crackdown continues, it will likely radicalize certain elements of the group and could herald a new, unwelcome era of armed Islamist insurgency.

The crackdown had been in the cards for weeks — ever since July 24, when military chief and Deputy Prime Minister Abdul Fattah al-Sisi called for mass popular demonstrations to support and “authorize” the police and army to deal with the Brotherhood. The crowds turned out and tensions deepened. A flurry of failed diplomatic bids by the U.S., the E.U. and others found little success.

There were never any serious indications that a brokered resolution was possible, and it’s likely that neither side tried particularly hard to reach an accord. The Brotherhood accused the government of seeking an excuse to wipe their organization from the political map, while the military-backed government accused the Brotherhood of cynically trying to provoke violence in order to create new martyrs to the cause.

On each side, the redline was Morsi — currently in his sixth week of military custody in an undisclosed location. Mansour’s government insisted that any resolution started with the Brotherhood accepting its place in Egypt’s new reality and giving up their hope that Morsi could return as President. The Brotherhood repeatedly dangled the prospect of fresh presidential elections, but insisted that those negotiations begin with Morsi’s return to power. Late last week, interim President Mansour officially reported that negotiations had failed and blamed the Brotherhood for their intransigence.

— With reporting by Jay Newton-Small / Washington

Khalil is a Cairo-based journalist and author of Liberation Square: Inside the Egyptian Revolution and the Rebirth of a Nation